In migratory species, sexual size dimorphism can mean differing energetic requirements for males and females. Differences in the costs of migration and in the environmental conditions occurring throughout the range may therefore result in sex-biases in distribution and resource use at different spatial scales. In order to identify the scale at which sexual segregation operates, and thus the scale at which environmental changes may have sex-biased impacts, we use range-wide tracking of individually color-ringed Icelandic black-tailed godwits (Limosa limosa islandica) to quantify sexual segregation at scales ranging from the occupation of sites throughout the non-breeding range to within-site differences in distribution and resource use. Throughout the range of this migratory shorebird, there is no evidence of large-scale sex differences in distribution during the non-breeding season. However, the sexes differ in their selection of prey types and sizes, which results in small-scale sexual segregation within estuaries. The scale of sexual segregation therefore depends on the scale of variation in resource distribution, which, in this system, is primarily within estuaries. Sexual segregation in within-site distribution and resource use means that local-scale anthropogenic impacts on estuarine benthic prey communities may disproportionately affect the sexes in these migratory shorebirds.